all non reression tests pass

nonregressions/volumes/esrf_scans/esynth/batch_extraction_esynth1.py

@@ -11,12 +11,13 @@ from XRStools import xrs_read,  xrs_rois
 
 import os
 def main():    
-    os.system("xz -dk mask.h5.xz --stdout > mask.h5")
+    os.system("xz -dk ../mask.h5.xz --stdout > mask.h5")
+
     filter_path = "mask.h5:/FILTER_MASK/filter"
 
     roi_scan_num   = [245,246,247]
     reference_scan_list = [245, 246, 247]
-    
+
     monitor_column = "izero/0.000001"
     
     first_scan_num = 651 
@@ -56,7 +57,7 @@ def main():
 
         "do_step_scalars"               :    False,
     
-        "do_step_interpolation_coefficients":    True,
+        "do_step_interpolation_coefficients":    False,
         
         "do_step_finalise_for_fit":              True
     }
@@ -138,6 +139,8 @@ def main():
     )
     
     
+            
+            
 main()
 
 

nonregressions/volumes/esrf_scans/interpolation/batch_extraction_interp.py

@@ -5,7 +5,7 @@ import json
 import os
 import h5py
 import math
-from XRStools import tools_sequencer_interp
+from XRStools import tools_sequencer_interp, xrs_rois, xrs_read
 import os
 def main():    
     os.system("xz -dk ../mask.h5.xz --stdout > mask.h5 ")
@@ -37,26 +37,28 @@ def main():
         ["niter_global"  , 3  ]
     ])                                 
 
-    resynth_z_square = 0
+    resynth_z_square = 0.0
 
-    selected_rois = list(range(0,24)) + list( range(36,60) ) 
+    # selected_rois = list(range(0,24)) + list( range(36,60) ) 
+    selected_rois = list(range(24,36)) + list( range(60,72) ) 
 
-    scal_prod_use_optional_solution = True 
+    scal_prod_use_optional_solution = False
 
-    volume_retrieval_beta  = 6.0e-20
+    volume_retrieval_beta  = 6.0e-1
     volume_retrieval_niter = 100 
     
     
     steps_to_do = {
         "do_step_make_roi":                      False,
-        "do_step_sample_extraction":             True,
+        "do_step_sample_extraction":             False,
         "do_step_interpolation":                 False,
         "do_step_extract_reference_scan":             False,
                 
         "do_step_fit_reference_response":               False,
         "do_step_resynthetise_reference":               False,
-        "do_step_scalars"               :    True,
-        "do_step_volume_retrieval"      :    False,
+        "do_step_scalars"               :    False,
+        "do_step_volume_retrieval"      :    True,
+        "do_step_put_all_in_one_stack"  : True
     }
 
     
@@ -81,17 +83,19 @@ def main():
     ######  LOADING PEAKS SHIFTS
     ###### peaks_shifts = h5py.File("../peaks_positions_for_analysers.h5","r")["peaks_positions"][()]
     ###### assert( len(peaks_shifts) == 72)
-    
-    roiob = xrs_rois.roi_object()
-    roiob.loadH5( roi_target_path  )
-    elastic = xrs_read.Hydra( datadir )
-    elastic.set_roiObj( roiob )
-    elastic.get_compensation_factor( elastic_scan_for_peaks_shifts , method='sum')
-    el_dict = elastic.cenom_dict
-    Enominal = np.median(  list( el_dict.values() ) )
-    peaks_shift = np.array([    el_dict["ROI%02d"%i] if ("ROI%02d"%i) in  el_dict else nan    for i in range 72  ] ) 
-    Enominal = np.median(peaks_shifts)
-    peaks_shifts-= Enominal
+    if steps_to_do["do_step_interpolation"]:
+        roiob = xrs_rois.roi_object()
+        roiob.loadH5( roi_target_path  )
+        elastic = xrs_read.Hydra( datadir )
+        elastic.set_roiObj( roiob )
+        elastic.get_compensation_factor( elastic_scan_for_peaks_shifts , method='sum')
+        el_dict = elastic.cenom_dict
+        Enominal = np.median(  list( el_dict.values() ) )
+        peaks_shifts = np.array([    el_dict["ROI%02d"%i] if ("ROI%02d"%i) in  el_dict else nan    for i in range( 72)  ] ) 
+        Enominal = np.median(peaks_shifts)
+        peaks_shifts-= Enominal
+    else:
+        peaks_shifts = None
     
     ##############################################################
     ##########################################################################
@@ -121,7 +125,7 @@ def main():
                       response_fit_options = response_fit_options,
                       
                       resynthetised_reference_and_roi_target_file = resynthetised_reference_and_roi_target_file,
-                      resynth_z_square = 0
+                                             resynth_z_square = 0,
 
                       selected_rois = selected_rois,
                       
@@ -135,6 +139,25 @@ def main():
     
     
 
+    if steps_to_do["do_step_put_all_in_one_stack"] :
+
+        volumefile  = scalar_products_and_volume_target_file
+
+        h5file_root = h5py.File( volumefile ,"r+" )
+
+        scankeys = list( h5file_root.keys())
+        scankeys.sort()
+        volumes = []
+        for k in scankeys:
+            if k[:1]!="_":
+                continue
+            print( k)
+            if "volume" in h5file_root[k]:
+                volumes.append( h5file_root[k]["volume"]  )
+        # volume = np.concatenate(volumes,axis=0)
+        volume = np.array(volumes)
+        h5py.File("concatenated_volume.h5","w")["volume"] = volume
+        h5file_root.close()
             
             
 main()